CohortMethod
Comparative Cohort Method with Large Scale Propensity and Outcome Models
Description
Functions for performing comparative cohort studies in an observational database in the Observational Medical Outcomes Partnership (OMOP) Common Data Model. Can extract all necessary data from a database. This implements large-scale propensity scores (LSPS) as described in Tian et al. (2018) <doi:10.1093/ije/dyy120>, using a large set of covariates, including for example all drugs, diagnoses, procedures, as well as age, comorbidity indexes, etc. Large scale regularized regression is used to fit the propensity and outcome models as described in Suchard et al. (2013) <doi:10.1145/2414416.2414791>. Functions are included for trimming, stratifying, (variable and fixed ratio) matching and weighting by propensity scores, as well as diagnostic functions, such as propensity score distribution plots and plots showing covariate balance before and after matching and/or trimming. Supported outcome models are (conditional) logistic regression, (conditional) Poisson regression, and (stratified) Cox regression. Also included are Kaplan-Meier plots that can adjust for the stratification or matching.
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Last 90 days
2K
Last year
Trend: +5% (30d vs prior 30d)
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Last 90 days
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Trend: -33.9% (30d vs prior 30d)
CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 27, 2026
ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 19, 2026
tests
Running ‘testthat.R’ [227s/324s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> test_check("CohortMethod")
Loading required package: CohortMethod
Loading required package: DatabaseConnector
Loading re
...[truncated]...
cannot use a variable created in the same `summarise()`.
✖ `sum` was created earlier in this `summarise()`.
ℹ You need an extra `mutate()` step to use it.
[ FAIL 6 | WARN 2 | SKIP 1 | PASS 433 ]
Error:
! Test failures.
Execution halted
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026
ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026
package dependencies
Packages required but not available: 'DatabaseConnector', 'Cyclops', 'FeatureExtraction', 'Andromeda' Packages suggested but not available for checking: 'Eunomia', 'ResultModelManager' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 24, 2026
ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE May 17, 2026
package dependencies
Packages required but not available: 'Cyclops', 'FeatureExtraction', 'Andromeda' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 15, 2026
ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE May 13, 2026
package dependencies
Packages required but not available: 'Cyclops', 'FeatureExtraction', 'Andromeda' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 22, 2026
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 18, 2026
whether package can be installed
Installation failed. See 'd:/Rcompile/CRANpkg/local/4.6/CohortMethod.Rcheck/00install.out' for details.
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 6, 2026
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 3, 2026
package dependencies
Packages required but not available: 'DatabaseConnector', 'FeatureExtraction', 'SqlRender' Packages suggested but not available for checking: 'Eunomia', 'ResultModelManager' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
OK 6 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 21, 2026
Code
Structure
Lines of code
19,568
Files
147
Compiled share
4%
Has compiled src
Yes
Language breakdown
API
Exported functions
66
Internal functions
97
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.38
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
87.9%
\dontrun example ratio
0%
Roxygen coverage
100%
Has pkgdown
No
NEWS present
Yes
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
20%
Unsafe pattern score
0
Dep constraint coverage
31.8%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
1
C++ standard
–
License
Apache License 2.0
License flags
SPDX valid, OSI approved
History
Versions
3
First release
2026-03-21
Latest release
2026-06-22
Avg cadence
47 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.